add last question corrections for TP1

Practical1/Correction/Q5_SalmonIndex.nf

@@ -0,0 +1,21 @@
+nextflow.enable.dsl=2
+
+params.ref = "ref.fa"
+refch = file(params.ref)
+
+process buildIndex(){
+	input:
+		path ref
+	output:
+		path "transcripts_index"
+	publishDir "index", mode: "copy"
+	shell:
+	'''
+	salmon index -t !{ref} -i transcripts_index
+	'''
+}
+
+workflow {
+   buildIndex(refch)
+}
+

Practical1/Correction/Q6_Salmon.nf

@@ -0,0 +1,38 @@
+nextflow.enable.dsl=2
+
+params.ref = "ref.fa"
+params.input = "fastq/"
+
+refch = file(params.ref)
+fastqch = channel.fromFilePairs("${params.input}/*_{1,2}.fastq.gz")
+
+process buildIndex(){
+	input:
+		path ref
+	output:
+		path "transcripts_index"
+	publishDir "index", mode: "copy"
+	shell:
+	'''
+	salmon index -t !{ref} -i transcripts_index
+	'''
+}
+
+process quant(){
+	input:
+		path index
+		tuple val(ID), path(fastq)
+	output:
+		path "${ID}"
+	publishDir "expression", mode: "copy"
+	shell:
+        '''
+        salmon quant -i !{index} -l A -1 !{fastq[0]} -2 !{fastq[1]} -o !{ID}
+        '''
+}
+
+workflow {
+   buildIndex(refch)
+   quant( buildIndex.out, fastqch)
+}
+

Practical1/Correction/Q8_Salmon_SRA.nf

@@ -0,0 +1,38 @@
+nextflow.enable.dsl=2
+
+params.ref = "ref.fa"
+params.input = "fastq/"
+
+refch = file(params.ref)
+fastqch = channel.fromSRA("SRP156394")
+
+process buildIndex(){
+	input:
+		path ref
+	output:
+		path "transcripts_index"
+	publishDir "index", mode: "copy"
+	shell:
+	'''
+	salmon index -t !{ref} -i transcripts_index
+	'''
+}
+
+process quant(){
+	input:
+		path index
+		tuple val(ID), path(fastq)
+	output:
+		path "${ID}"
+	publishDir "expression", mode: "copy"
+	shell:
+        '''
+        salmon quant -i !{index} -l A -1 !{fastq[0]} -2 !{fastq[1]} -o !{ID}
+        '''
+}
+
+workflow {
+   buildIndex(refch)
+   quant( buildIndex.out, fastqch)
+}
+

Practical1/Correction/Q8_Salmon_pimped.nf

@@ -0,0 +1,48 @@
+nextflow.enable.dsl=2
+
+params.index = null
+params.ref = "ref.fa"
+params.input = "fastq/"
+params.cpus = 2
+params.memory = 5
+
+refch = file(params.ref)
+fastqch = channel.fromFilePairs("${params.input}/*_{1,2}.fastq.gz")
+
+process buildIndex(){
+	input:
+		path ref
+	output:
+		path "transcripts_index"
+	publishDir "index", mode: "copy"
+	shell:
+	'''
+	salmon index -t !{ref} -i transcripts_index
+	'''
+}
+
+process quant(){
+	cpus params.cpus
+	memory params.memory+"GB"
+
+	input:
+		path index
+		tuple val(ID), path(fastq)
+	output:
+		path "${ID}"
+	publishDir "expression", mode: "copy"
+	shell:
+        '''
+        salmon quant -i !{index} -l A -1 !{fastq[0]} -2 !{fastq[1]} -o !{ID}
+        '''
+}
+
+workflow {
+   if(!params.index){
+     ind = buildIndex(refch)
+   }else{
+     ind = channel.from(params.ref)
+   }
+   quant( ind, fastqch)
+}
+